they would still play differently. physics wise DS would be easier to knock away - she/it generally levitates, so, like mewtwo, would be easier to hit away. she would also have a slower fastfall (she levitates, impying some form of antigravity ability). it is noted in all apearances she moves medium speed, but as very fast dodges and what would probably be considered rolls. it is noted that attack wise, she would have different skills (though probably a variant of the basic charge shot) but other than that uses more or less completely different attacks (boost ball, phazon scattershot, etc). even if you havent played any of the games, after a few plays at dark samus it would be notable that even if she was added as a clone(hopefully they wont if they add at all, but it could still happen) she could play very differently.
Looks wise of course, other than stature/movement/colouring she isn't a whole lot visually different, so yes people who have never played the games (and when brawl is out, do not play her if she/it is in) will probably think clone. My belief is that unless she is intentionally added as a close-molded clone, it would take but a few plays to see how very different she/it would be.